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Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress - PubMed

  • ️Sat Jan 01 2022

Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress

Irfan Ali Sabir et al. Front Plant Sci. 2022.

Abstract

The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus avium L., F. vesca, and P. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the PavGAox genes have a remarkably well-maintained exon-intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation, PavGAox genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in Prunus avium L., F. vesca, and P. mume revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of cis-regulatory elements in the upstream region of the 140 PavGAox members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the PavGAox genes display a variety of tissue expression patterns in diverse tissues, with most of the PavGAox genes displaying tissue-specific expression patterns. Furthermore, most of the PavGAox genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of PavGAox genes are responsible for maintaining the GA level in plant-like Pav co4017001.1 g010.1.br, Pav sc0000024.1 g340.1.br, and Pav sc0000024.1 g270.1.mk. The subcellular localization of PavGAox protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family's interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.

Keywords: PavGAox; characterization; gene duplication; qRT-PCR; subcellular localization.

Copyright © 2022 Sabir, Manzoor, Shah, Abbas, Liu, Fiaz, Shah, Jiu, Wang, Abdullah and Zhang.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1

Phylogenetic tree of GAox protein of P. avium, P. mume, F. vesca, and A. thaliana. Each color representing a subfamily (A–F) of GAox genes. Green, red, and light blue bars indicate length of amino acids, intron, and domain numbers, respectively. The phylogenetic tree was constructed with the itol software.

FIGURE 2
FIGURE 2

Phylogenic relationships and conserved protein motif composition for GAox family proteins in sweet cherry. The motif composition of PavGaox protein (1–20) is indicated by different colored boxes with specific motif numbers, and figure legends are mentioned on the top.

FIGURE 3
FIGURE 3

Phylogenic relationships and gene structure for GAox family proteins in sweet cherry. The relative position and size of the exon can be estimated using the scale at the bottom. Blue boxes, black lines, and red boxes represent exons, introns, and UTR, respectively.

FIGURE 4
FIGURE 4

Collinearity relationship of GAox genes in P. avium and other Rosaceae species. Pa, Pp, Pm, and Fv indicate P. avium, P. persica, P. mume, and F. vesca, respectively.

FIGURE 5
FIGURE 5

Prunus avium, Prunus mume, Prunus persica, and Pyrus bretschneideri have gene duplication and chromosomal localization. A colorful line links duplicated gene pairs.

FIGURE 6
FIGURE 6

Ka/Ks values of GAox gene family in three Rosaceae species. Comparison of Ka/Ks values for different modes of gene duplications. WGD, whole-genome duplication; PD, proximal duplication; TRD, transposed duplication; TD, tandem duplication; DSD, dispersed duplication.

FIGURE 7
FIGURE 7

Gene ontology (GO) annotation of PvGAox proteins. The GO annotation was achieved based on three categories, biological process (BP), molecular function (MF), and cellular component (CC). The numbers on the abscissa show the number of predicted proteins.

FIGURE 8
FIGURE 8

Predicted cis-elements in the promoter regions of the PavGAox genes. All promoter sequences (2 kb) were analyzed. The PavGAox genes are shown on the left side of the figure. The scale bar at the bottom indicates the length of promoter sequence.

FIGURE 9
FIGURE 9

Transcriptomic analysis of 140 PavGaox genes in different dormancy-related phase data (organogenesis, paradormancy, endodormancy, ecodormancy, and dormancy release). Red, black, and green represent high, low, and no expression levels, respectively.

FIGURE 10
FIGURE 10

Relative expression patterns of PavGAox genes through qRT-PCR on different tissues (bud, flower, and fruit). Mean ± SE of three biological replicates (each having three technical replicates).

FIGURE 11
FIGURE 11

Expression profiles of selected PavGaox genes on the bud before (control) or 1D, 3D, and 6D after treatment with prohexadione calcium. Mean ± SE of three biological replicates (each having three technical replicates).

FIGURE 12
FIGURE 12

Expression profiles of selected PavGaox genes on the bud before (control) or 1D, 3D, and 6D after treatment with GA. Mean ± SE of three biological replicates (each having three technical replicates).

FIGURE 13
FIGURE 13

Subcellular localization of Pav_sc0000465.1_g550.1.mk in tobacco epidermal cells. Transient expression of Pav_sc0000465.1_g550.1.mk was investigated in epidermal cells of tobacco using a confocal microscope. For the subcellular localization of p35S:: Pav_sc0000465.1_g550.1.mk: eGFP, recombinants were detected by Agrobacterium-mediated infiltration.

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References

    1. Abdullah M., Cao Y., Cheng X., Meng D., Chen Y., Shakoor A., et al. (2018a). The sucrose synthase gene family in Chinese pear (Pyrus bretschneideri Rehd.): structure, expression, and evolution. Molecules 23:1144. 10.3390/molecules23051144 - DOI - PMC - PubMed
    1. Abdullah M., Cheng X., Cao Y., Su X., Manzoor M. A., Gao J., et al. (2018b). Zinc finger-homeodomain transcriptional factors (ZHDs) in upland cotton (Gossypium hirsutum): genome-wide identification and expression analysis in fiber development. Front. Genet. 9:357. 10.3389/fgene.2018.00357 - DOI - PMC - PubMed
    1. Alvarez-Buylla E. R., Liljegren S. J., Pelaz S., Gold S. E., Burgeff C., Ditta G. S., et al. (2000). MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J. 24 457–466. 10.1046/j.1365-313x.2000.00891.x - DOI - PubMed
    1. Atkinson C. J., Brennan R. M., Jones H. G. (2013). Declining chilling and its impact on temperate perennial crops. Environ. Exp. Bot. 91 48–62.
    1. Ayele B. T., Ozga J. A., Kurepin L. V., Reinecke D. M. (2006). Developmental and embryo axis regulation of gibberellin biosynthesis during germination and young seedling growth of pea. Plant Physiol. 142 1267–1281. 10.1104/pp.106.086199 - DOI - PMC - PubMed

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